chr12-23061041-C-T

Position:

• chr12-23061041-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000538317.6(LINC02955):​n.1271+3144C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0777 in 151,926 control chromosomes in the GnomAD database, including 640 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.078 (640 hom., cov: 32)
• Consequence: LINC02955 ENST00000538317.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249

Genes affected

LINC02955 (HGNC:55973): (long intergenic non-protein coding RNA 2955)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02955	ENST00000538317.6	n.1271+3144C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0777 AC: 11788 AN: 151806 Hom.: 638 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0503

Gnomad ASJ AF: 0.0833

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.0823

Gnomad MID AF: 0.0481

Gnomad NFE AF: 0.0376

Gnomad OTH AF: 0.0503

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0777 AC: 11811 AN: 151926 Hom.: 640 Cov.: 32 AF XY: 0.0818 AC XY: 6069 AN XY: 74232

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.0507

Gnomad4 ASJ AF: 0.0833

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.0823

Gnomad4 NFE AF: 0.0376

Gnomad4 OTH AF: 0.0531

Alfa AF: 0.0495 Hom.: 58

Bravo AF: 0.0759

Asia WGS AF: 0.191 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	14
DANN	Benign	0.59

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12580249; hg19: chr12-23213975;